NFASC p.Ser901=
c.2703C>T · rs142292676 · VCV2639842
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.419%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.106 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6 | GERP -4.6 |
| Overall | ||
| CADD | 8.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.419%
South Asian · 382/91,082 alleles
Filtering AF
0.385%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.371%
Overall
0.0475%
766/1,614,216 alleles · rare
exomes 704/1,461,868 · genomes 62/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.419% | 238 |
| Middle Eastern | 0.148% | 674 |
| Remaining individualsnot grpmax-eligible | 0.0688% | 1,454 |
| Admixed American | 0.06% | 1,668 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0338% | 2,961 |
| African / African-American | 0.0306% | 3,263 |
| European (non-Finnish) | 0.022% | 4,539 |
| East Asian | 0.00446% | 22,442 |
| Finnishnot grpmax-eligible | 0.00156% | 64,042 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NFASC
- Protein
- p.Ser901=
- Coding
- c.2703C>T
- MANE Select
- NM_001005388
- dbSNP
- rs142292676
- Type
- single nucleotide variant
- Location
- chr1:204988742 (GRCh38)
- Gene constraint
- LOEUF 0.362 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.23 · 2 PDB
- Residue 901
- the fibronectin type-iii 3 domain; a UniProt-annotated variant site (in nedcpmd; uncertain significance; no protein expression)
Similar variants
- NFASC c.2593+5G>A Uncertain significance ★★ same type
- NFASC p.Ala253Thr Uncertain significance ★★ same type
- NFASC p.Arg133His Uncertain significance ★★ same type
- NFASC p.Arg436Gln Uncertain significance ★★ same type
- NFASC p.Asn655Asp Uncertain significance ★★ same type
- NFASC p.Asp1038Ala Uncertain significance ★★ same type
- NFASC p.Asp601Val Uncertain significance ★★ same type
- NFASC p.Gly23Arg Uncertain significance ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nfasc-p-ser901 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown